# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 16:32:13 2022
#   Inital geometry file: a 118 line input string
#   Ligand name: [(3S)-3-(1H-benzimidazol-2-yl)piperidin-1-yl](2-methyl-1-benzofuran-5-yl)methanone
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1oc2ccc(cc2c1)C(=O)N3CCC[C@@H](C3)c4[nH]c5ccccc5n4
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 756  756  '[(3S)-3-(1H-benzimidazol-2-yl)piperidin-1-yl](2-methyl-1-benzofuran-5-yl)methanone'  ligand  48  27  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_756
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 756  O1   O  O     0  -0.484  -0.6776   1.9965   0.3472
 756  C9   C  C     0   0.518  -1.1221   0.8709   0.1625
 756  C5   C  CR6   0  -0.081  -2.5914   0.6886  -0.0454
 756  C4   C  CR16  0  -0.355  -3.3141  -0.2129   0.7262
 756  C6   C  CR16  0  -0.289  -3.2402   1.5391  -0.9530
 756  C7   C  CR16  0  -0.335  -4.6118   1.4900  -1.1367
 756  C8   C  CR56  0   0.356  -5.3076   0.5836  -0.3578
 756  C3   C  CR56  0   0.088  -4.6966  -0.2619   0.5713
 756  C2   C  CR15  0  -0.425  -5.7678  -1.0163   1.1585
 756  O    O  O     0  -0.454  -6.6410   0.3806  -0.3599
 756  C1   C  CR5   0   0.370  -6.9036  -0.5909   0.5638
 756  C    C  CH3   0  -0.754  -8.3202  -0.9774   0.7375
 756  N    N  NT    0  -0.455  -0.3444  -0.2371   0.1908
 756  C14  C  CH2   0  -0.291   1.0582  -0.1164   0.5398
 756  C13  C  CH1   0  -0.394   1.9438  -0.2075  -0.7108
 756  C12  C  CH2   0  -0.428   1.6556  -1.5150  -1.4575
 756  C11  C  CH2   0  -0.438   0.1658  -1.6507  -1.7410
 756  C10  C  CH2   0  -0.321  -0.6666  -1.4933  -0.4743
 756  C15  C  CR5   0   0.488   3.3842  -0.0505  -0.3630
 756  N2   N  NR15  0  -0.704   4.0582  -0.9540   0.4008
 756  C21  C  CR56  0   0.334   5.3455  -0.5055   0.5341
 756  C16  C  CR56  0   0.136   5.3754   0.6982  -0.1886
 756  N1   N  N     0  -0.475   4.1372   0.9501  -0.7323
 756  C20  C  CR16  0  -0.311   6.4591  -1.0117   1.1939
 756  C19  C  CR16  0  -0.279   7.6232  -0.2668   1.1076
 756  C18  C  CR16  0  -0.272   7.6727   0.9373   0.3888
 756  C17  C  CR16  0  -0.338   6.5581   1.4332  -0.2644
 756  H1   H  HCR6  0   0.270  -2.8188  -0.8553   1.4443
 756  H2   H  HCR6  0   0.263  -2.6563   2.2441  -1.5297
 756  H3   H  HCR6  0   0.273  -5.1098   2.1352  -1.8483
 756  H4   H  HCR5  0   0.266  -5.7011  -1.7759   1.9205
 756  H5   H  HCH3  0   0.262  -8.9245  -0.1330   1.0742
 756  H6   H  HCH3  0   0.262  -8.7529  -1.3412  -0.1958
 756  H7   H  HCH3  0   0.263  -8.3981  -1.7683   1.4800
 756  H8   H  HCH2  0   0.278   1.2254   0.8205   1.0647
 756  H9   H  HCH2  0   0.249   1.2995  -0.9299   1.2320
 756  H10  H  HCH1  0   0.275   1.6984   0.6347  -1.3636
 756  H11  H  HCH2  0   0.259   2.2257  -1.5435  -2.3877
 756  H12  H  HCH2  0   0.225   1.9875  -2.3711  -0.8606
 756  H13  H  HCH2  0   0.232  -0.1457  -0.8955  -2.4688
 756  H14  H  HCH2  0   0.250  -0.0453  -2.6265  -2.1824
 756  H15  H  HCH2  0   0.246  -0.4649  -2.3155   0.2187
 756  H16  H  HCH2  0   0.278  -1.7234  -1.5329  -0.7200
 756  H17  H  HNR5  0   0.417   3.6865  -1.8060   0.7896
 756  H19  H  HCR6  0   0.265   6.4226  -1.9396   1.7494
 756  H20  H  HCR6  0   0.255   8.5155  -0.6212   1.6069
 756  H21  H  HCR6  0   0.252   8.6042   1.4865   0.3445
 756  H22  H  HCR6  0   0.253   6.5990   2.3627  -0.8179

loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
_chem_comp_bond.value_dist_neutron
 756  C19  C18  aromatic  1.403  0.020  1.403
 756  C19  C20  aromatic  1.385  0.020  1.385
 756  C18  C17  aromatic  1.384  0.020  1.384
 756  C20  C21  aromatic  1.390  0.020  1.390
 756  C17  C16  aromatic  1.395  0.020  1.395
 756  C21  C16  aromatic  1.404  0.020  1.404
 756  C21  N2   aromatic  1.370  0.020  1.370
 756  C16  N1   aromatic  1.376  0.020  1.376
 756  N2   C15  aromatic  1.362  0.020  1.362
 756  N1   C15  aromatic  1.306  0.020  1.306
 756  C15  C13  single    1.490  0.020  1.490
 756  C12  C13  single    1.533  0.020  1.533
 756  C12  C11  single    1.523  0.020  1.523
 756  C13  C14  single    1.535  0.020  1.535
 756  C11  C10  single    1.524  0.020  1.524
 756  C14  N    single    1.450  0.020  1.450
 756  C10  N    single    1.457  0.020  1.457
 756  N    C9   single    1.354  0.020  1.354
 756  C4   C3   aromatic  1.392  0.020  1.392
 756  C4   C5   aromatic  1.389  0.020  1.389
 756  C2   C3   aromatic  1.436  0.020  1.436
 756  C2   C1   aromatic  1.351  0.020  1.351
 756  C9   C5   single    1.495  0.020  1.495
 756  C9   O1   double    1.224  0.020  1.224
 756  C3   C8   aromatic  1.397  0.020  1.397
 756  C5   C6   aromatic  1.403  0.020  1.403
 756  C1   C    single    1.479  0.020  1.479
 756  C1   O    aromatic  1.366  0.020  1.366
 756  C8   O    aromatic  1.349  0.020  1.349
 756  C8   C7   aromatic  1.383  0.020  1.383
 756  C6   C7   aromatic  1.385  0.020  1.385
 756  C4   H1   single    0.930  0.020  1.080
 756  C6   H2   single    0.930  0.020  1.080
 756  C7   H3   single    0.930  0.020  1.080
 756  C2   H4   single    0.930  0.020  1.080
 756  C    H5   single    0.970  0.020  1.090
 756  C    H6   single    0.970  0.020  1.090
 756  C    H7   single    0.970  0.020  1.090
 756  C14  H8   single    0.970  0.020  1.090
 756  C14  H9   single    0.970  0.020  1.090
 756  C13  H10  single    0.970  0.020  1.090
 756  C12  H11  single    0.970  0.020  1.090
 756  C12  H12  single    0.970  0.020  1.090
 756  C11  H13  single    0.970  0.020  1.090
 756  C11  H14  single    0.970  0.020  1.090
 756  C10  H15  single    0.970  0.020  1.090
 756  C10  H16  single    0.970  0.020  1.090
 756  N2   H17  single    0.860  0.020  1.020
 756  C20  H19  single    0.930  0.020  1.080
 756  C19  H20  single    0.930  0.020  1.080
 756  C18  H21  single    0.930  0.020  1.080
 756  C17  H22  single    0.930  0.020  1.080

loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
 756  N    C9   C5   117.88  3.000
 756  C5   C9   O1   119.33  3.000
 756  N    C9   O1   122.73  3.000
 756  C6   C5   C4   120.81  3.000
 756  C6   C5   C9   118.07  3.000
 756  C4   C5   C9   120.87  3.000
 756  H1   C4   C3   120.46  3.000
 756  H1   C4   C5   121.00  3.000
 756  C3   C4   C5   118.53  3.000
 756  H2   C6   C7   119.13  3.000
 756  H2   C6   C5   119.37  3.000
 756  C7   C6   C5   121.50  3.000
 756  H3   C7   C8   121.98  3.000
 756  H3   C7   C6   121.48  3.000
 756  C8   C7   C6   116.54  3.000
 756  O    C8   C3   110.02  3.000
 756  O    C8   C7   126.52  3.000
 756  C3   C8   C7   123.45  3.000
 756  C2   C3   C8   105.29  3.000
 756  C8   C3   C4   119.15  3.000
 756  C2   C3   C4   135.56  3.000
 756  H4   C2   C1   125.81  3.000
 756  H4   C2   C3   127.82  3.000
 756  C1   C2   C3   106.37  3.000
 756  C1   O    C8   107.22  3.000
 756  C    C1   O    116.71  3.000
 756  O    C1   C2   111.10  3.000
 756  C    C1   C2   132.19  3.000
 756  H7   C    H6   108.24  3.000
 756  H7   C    H5   108.20  3.000
 756  H6   C    H5   107.60  3.000
 756  H7   C    C1   109.81  3.000
 756  H6   C    C1   111.50  3.000
 756  H5   C    C1   111.37  3.000
 756  C10  N    C14  113.28  3.000
 756  C10  N    C9   124.67  3.000
 756  C14  N    C9   119.50  3.000
 756  H9   C14  H8   107.53  3.000
 756  H9   C14  C13  110.11  3.000
 756  H8   C14  C13  110.84  3.000
 756  H9   C14  N    107.66  3.000
 756  H8   C14  N    109.67  3.000
 756  C13  C14  N    110.92  3.000
 756  H10  C13  C15  105.97  3.000
 756  H10  C13  C12  108.91  3.000
 756  C15  C13  C12  112.66  3.000
 756  H10  C13  C14  108.13  3.000
 756  C12  C13  C14  109.81  3.000
 756  C15  C13  C14  111.18  3.000
 756  H12  C12  H11  106.61  3.000
 756  H12  C12  C11  109.17  3.000
 756  H11  C12  C11  110.49  3.000
 756  H12  C12  C13  110.14  3.000
 756  H11  C12  C13  109.82  3.000
 756  C11  C12  C13  110.53  3.000
 756  H14  C11  H13  107.04  3.000
 756  H14  C11  C10  108.83  3.000
 756  H13  C11  C10  109.04  3.000
 756  H14  C11  C12  110.13  3.000
 756  H13  C11  C12  109.94  3.000
 756  C10  C11  C12  111.74  3.000
 756  H16  C10  H15  107.18  3.000
 756  H16  C10  C11  109.86  3.000
 756  H15  C10  C11  110.38  3.000
 756  H16  C10  N    110.48  3.000
 756  H15  C10  N    108.54  3.000
 756  C11  C10  N    110.34  3.000
 756  N1   C15  N2   112.44  3.000
 756  N1   C15  C13  124.91  3.000
 756  N2   C15  C13  122.66  3.000
 756  H17  N2   C21  125.88  3.000
 756  H17  N2   C15  126.50  3.000
 756  C21  N2   C15  107.61  3.000
 756  C20  C21  C16  122.64  3.000
 756  C16  C21  N2   104.51  3.000
 756  C20  C21  N2   132.85  3.000
 756  C17  C16  N1   130.19  3.000
 756  N1   C16  C21  109.95  3.000
 756  C17  C16  C21  119.86  3.000
 756  C16  N1   C15  105.49  3.000
 756  H19  C20  C19  121.44  3.000
 756  H19  C20  C21  121.94  3.000
 756  C19  C20  C21  116.63  3.000
 756  H20  C19  C18  119.23  3.000
 756  H20  C19  C20  119.23  3.000
 756  C18  C19  C20  121.55  3.000
 756  H21  C18  C17  119.48  3.000
 756  H21  C18  C19  119.13  3.000
 756  C17  C18  C19  121.39  3.000
 756  H22  C17  C18  121.24  3.000
 756  H22  C17  C16  120.82  3.000
 756  C18  C17  C16  117.94  3.000

loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
 756  CONST_01  C2   C3   C4   C5   180.00   0.0  0
 756  CONST_02  C8   C3   C4   C5     0.00   0.0  0
 756  CONST_03  C8   C7   C6   C5     0.00   0.0  0
 756  CONST_04  C1   C2   C3   C4   180.00   0.0  0
 756  CONST_05  O    C8   C3   C4   180.00   0.0  0
 756  CONST_06  C7   C8   C3   C4     0.00   0.0  0
 756  CONST_07  C7   C6   C5   C4     0.00   0.0  0
 756  CONST_08  C3   C4   C5   C6     0.00   0.0  0
 756  CONST_09  C3   C8   C7   C6     0.00   0.0  0
 756  CONST_10  O    C8   C7   C6   180.00   0.0  0
 756  CONST_11  C2   C3   C8   C7   180.00   0.0  0
 756  CONST_12  C1   O    C8   C7   180.00   0.0  0
 756  CONST_13  C1   C2   C3   C8     0.00   0.0  0
 756  CONST_14  C2   C1   O    C8     0.00   0.0  0
 756  CONST_15  O    C1   C2   C3     0.00   0.0  0
 756  CONST_16  C1   O    C8   C3     0.00   0.0  0
 756  CONST_17  O    C8   C3   C2     0.00   0.0  0
 756  CONST_18  C20  C21  N2   C15  180.00   0.0  0
 756  CONST_19  C16  C21  N2   C15    0.00   0.0  0
 756  CONST_20  C17  C16  N1   C15  180.00   0.0  0
 756  CONST_21  C21  C16  N1   C15    0.00   0.0  0
 756  CONST_22  C19  C20  C21  N2   180.00   0.0  0
 756  CONST_23  C17  C16  C21  N2   180.00   0.0  0
 756  CONST_24  N1   C16  C21  N2     0.00   0.0  0
 756  CONST_25  C16  N1   C15  N2     0.00   0.0  0
 756  CONST_26  C18  C19  C20  C21    0.00   0.0  0
 756  CONST_27  C18  C17  C16  C21    0.00   0.0  0
 756  CONST_28  N1   C15  N2   C21    0.00   0.0  0
 756  CONST_29  C19  C18  C17  C16    0.00   0.0  0
 756  CONST_30  C19  C20  C21  C16    0.00   0.0  0
 756  CONST_31  C18  C17  C16  N1   180.00   0.0  0
 756  CONST_32  C20  C21  C16  N1   180.00   0.0  0
 756  CONST_33  C17  C18  C19  C20    0.00   0.0  0
 756  CONST_34  C17  C16  C21  C20    0.00   0.0  0
 756  CONST_35  C21  N2   C15  C13  180.00   0.0  0
 756  CONST_36  C16  N1   C15  C13  180.00   0.0  0
 756  CONST_37  C3   C4   C5   C9   180.00   0.0  0
 756  CONST_38  C7   C6   C5   C9   180.00   0.0  0
 756  CONST_39  C    C1   O    C8   180.00   0.0  0
 756  CONST_40  C    C1   C2   C3   180.00   0.0  0
 756  CONST_41  C14  N    C9   C5   180.00   0.0  0
 756  CONST_43  H3   C7   C6   C5   180.00   0.0  0
 756  CONST_44  H4   C2   C3   C4     0.00   0.0  0
 756  CONST_45  H2   C6   C5   C4   180.00   0.0  0
 756  CONST_46  H1   C4   C5   C6   180.00   0.0  0
 756  CONST_47  H17  N2   C15  C13    0.00   0.0  0
 756  CONST_48  H19  C20  C21  N2     0.00   0.0  0
 756  CONST_49  H20  C19  C20  C21  180.00   0.0  0
 756  CONST_50  H22  C17  C16  C21  180.00   0.0  0
 756  CONST_51  H21  C18  C17  C16  180.00   0.0  0
 756  CONST_52  C14  N    C9   O1     0.00   0.0  0
 756  Var_01    C12  C11  C10  N     54.42  30.0  1
 756  Var_02    C11  C10  N    C14  -57.95  30.0  1
 756  Var_03    C10  C11  C12  C13  -53.28  30.0  1
 756  Var_04    C10  N    C14  C13   59.43  30.0  1
 756  Var_05    N    C9   C5   C4    50.38  30.0  3
 756  Var_06    H5   C    C1   C2   118.43  30.0  2

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 756  chir_01  C13  C15  C12  C14  negativ

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 756  plan-1  C9   0.020
 756  plan-1  C5   0.020
 756  plan-1  C4   0.020
 756  plan-1  C6   0.020
 756  plan-1  C7   0.020
 756  plan-1  C8   0.020
 756  plan-1  C3   0.020
 756  plan-1  C2   0.020
 756  plan-1  O    0.020
 756  plan-1  C1   0.020
 756  plan-1  C    0.020
 756  plan-1  H1   0.020
 756  plan-1  H2   0.020
 756  plan-1  H3   0.020
 756  plan-1  H4   0.020
 756  plan-2  C13  0.020
 756  plan-2  C15  0.020
 756  plan-2  N2   0.020
 756  plan-2  C21  0.020
 756  plan-2  C16  0.020
 756  plan-2  N1   0.020
 756  plan-2  C20  0.020
 756  plan-2  C19  0.020
 756  plan-2  C18  0.020
 756  plan-2  C17  0.020
 756  plan-2  H17  0.020
 756  plan-2  H19  0.020
 756  plan-2  H20  0.020
 756  plan-2  H21  0.020
 756  plan-2  H22  0.020
 756  plan-3  O1   0.020
 756  plan-3  C9   0.020
 756  plan-3  C5   0.020
 756  plan-3  N    0.020
 756  plan-3  C14  0.020
 756  plan-3  C10  0.020

